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- PDB-5oqk: Solution NMR structure of truncated, human Hv1/VSOP (Voltage-gate... -

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Basic information

Entry
Database: PDB / ID: 5oqk
TitleSolution NMR structure of truncated, human Hv1/VSOP (Voltage-gated proton channel)
ComponentsVoltage-gated hydrogen channel 1
KeywordsPROTON TRANSPORT / voltage gated proton channel / anti-parallel four-helix bundle / membrane protein
Function / homology
Function and homology information


Sperm Motility And Taxes / voltage-gated proton channel activity / regulation of acrosome reaction / cellular response to pH / ROS and RNS production in phagocytes / voltage-gated monoatomic cation channel activity / response to pH / regulation of reactive oxygen species biosynthetic process / cellular response to zinc ion / monoatomic ion channel complex ...Sperm Motility And Taxes / voltage-gated proton channel activity / regulation of acrosome reaction / cellular response to pH / ROS and RNS production in phagocytes / voltage-gated monoatomic cation channel activity / response to pH / regulation of reactive oxygen species biosynthetic process / cellular response to zinc ion / monoatomic ion channel complex / response to zinc ion / single fertilization / sperm flagellum / specific granule membrane / cell redox homeostasis / proton transmembrane transport / secretory granule membrane / positive regulation of superoxide anion generation / regulation of intracellular pH / phagocytic vesicle membrane / apical plasma membrane / innate immune response / Neutrophil degranulation / protein homodimerization activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
Voltage-gated hydrogen channel 1, C-terminal membrane-localisation domain / Voltage-gated hydrogen channel 1 / C-terminal membrane-localisation domain of ion-channel, VCN1 / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Voltage-gated hydrogen channel 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBayrhuber, M. / Maslennikov, I. / Kwiatowski, W. / Sobol, A. / Wierschem, C. / Eichmann, C. / Riek, R.
CitationJournal: Biochemistry / Year: 2019
Title: Nuclear Magnetic Resonance Solution Structure and Functional Behavior of the Human Proton Channel.
Authors: Bayrhuber, M. / Maslennikov, I. / Kwiatkowski, W. / Sobol, A. / Wierschem, C. / Eichmann, C. / Frey, L. / Riek, R.
History
DepositionAug 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_nmr_spectrometer.model
Revision 1.2Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Voltage-gated hydrogen channel 1


Theoretical massNumber of molelcules
Total (without water)17,3521
Polymers17,3521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11350 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Voltage-gated hydrogen channel 1 / Hydrogen voltage-gated channel 1 / HV1 / Voltage sensor domain-only protein


Mass: 17352.062 Da / Num. of mol.: 1 / Fragment: UNP residues 82-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HVCN1, VSOP, UNQ578/PRO1140 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q96D96

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D HNCA
121isotropic23D HNCO
131isotropic23D HN(CA)CB
141isotropic23D 1H-15N NOESY
151isotropic23D 1H-13C NOESY

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Sample preparation

DetailsType: micelle
Contents: 0.4 mM [U-99% 13C; U-99% 15N; 50% 2H] Hv1/VSOP, 20 mM MES, 20 mM BisTris, 2 mM FC-12, 2 mM LDAO, 1 mM TCEP, 10 mM ZnCl2, 90% H2O/10% D2O
Label: sample-1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMHv1/VSOP[U-99% 13C; U-99% 15N; 50% 2H]1
20 mMMESnatural abundance1
20 mMBisTrisnatural abundance1
2 mMFC-12natural abundance1
2 mMLDAOnatural abundance1
1 mMTCEPnatural abundance1
10 mMZnCl2natural abundance1
Sample conditionsIonic strength: 30 mM / Label: conditions_1 / pH: 5.8 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR softwareName: CYANA / Developer: Guntert P. / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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